I'm new to 3d printing.. Just wondering if a model can be printed if it contains two seperate meshes (no moving stuff) Intersecting each other?. For example:- A long cylinder through a solid cube!..
I hope you get the idea. Sometimes properly fusing two parts of meshes with heavy details can be such a pain!.

Another question - Do I have to worry about mesh flow (triangles, faces with more than four edges.etc)?

In blender you can select the sphere and then the cylinder, export without joining the meshes, and shapeways will perform the boolean op on them.
Ngons in a mesh create a nonmanifold mesh, which cannot be printed. Triangles will work, as will quads for faces

Have any questions regarding Blender, and need fast answers, you are always welcome at the IRC Server Freenode, channel #blender. As a bonus, several there have experience in modelling for 3D prints.

A cautionary note to add (with solution).
Shapeways software will not boolean very small meshes together - the very small parts get removed instead.
The kind of size I'm talking about is what would be considered detail on FUD models and the removal by Shapeways software has not yet been resolved, however NetFabb Cloud Service has no issues booleaning any size parts together.